0s autopkgtest [02:29:46]: starting date and time: 2026-02-05 02:29:46+0000 0s autopkgtest [02:29:46]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:29:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dcnkqf82/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade bolt-lmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-20.secgroup --name adt-resolute-ppc64el-bolt-lmm-20260205-022944-juju-7f2275-prod-proposed-migration-environment-2-9c065d59-1f4d-49a7-8daf-b7b9d09fb696 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-ppc64el-bolt-lmm-20260205-022944-juju-7f2275-prod-proposed-migration-environment-2-9c065d59-1f4d-49a7-8daf-b7b9d09fb696 from image adt/ubuntu-resolute-ppc64el-server-20260205.img (UUID f866c950-0b62-4023-bac6-0f13279e15ed)... 69s autopkgtest [02:30:54]: testbed dpkg architecture: ppc64el 69s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 69s autopkgtest [02:30:54]: testbed apt version: 3.1.14 69s autopkgtest [02:30:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s autopkgtest [02:30:54]: testbed release detected to be: None 69s autopkgtest [02:30:55]: updating testbed package index (apt update) 69s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 69s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 70s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 70s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [257 kB] 70s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1449 kB] 70s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [21.6 kB] 70s Fetched 3839 kB in 1s (5522 kB/s) 71s Reading package lists... 72s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 72s Reading package lists... 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 73s The following packages will be upgraded: 73s libc-bin libc-gconv-modules-extra libc6 locales pollinate 73s python3-referencing sed 73s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Need to get 8612 kB of archives. 73s After this operation, 0 B of additional disk space will be used. 73s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el sed ppc64el 4.9-2build3 [211 kB] 73s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-gconv-modules-extra ppc64el 2.42-2ubuntu5 [1448 kB] 73s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc6 ppc64el 2.42-2ubuntu5 [1913 kB] 74s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libc-bin ppc64el 2.42-2ubuntu5 [748 kB] 74s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el locales all 2.42-2ubuntu5 [4255 kB] 74s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el pollinate all 4.33-4ubuntu5 [14.0 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 75s dpkg-preconfigure: unable to re-open stdin: No such file or directory 75s Fetched 8612 kB in 1s (7235 kB/s) 75s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 75s Preparing to unpack .../sed_4.9-2build3_ppc64el.deb ... 75s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 75s Setting up sed (4.9-2build3) ... 75s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 75s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_ppc64el.deb ... 75s Unpacking libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 75s Setting up libc-gconv-modules-extra:ppc64el (2.42-2ubuntu5) ... 75s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 75s Preparing to unpack .../libc6_2.42-2ubuntu5_ppc64el.deb ... 75s Unpacking libc6:ppc64el (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 76s Setting up libc6:ppc64el (2.42-2ubuntu5) ... 76s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 76s Preparing to unpack .../libc-bin_2.42-2ubuntu5_ppc64el.deb ... 76s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 76s Setting up libc-bin (2.42-2ubuntu5) ... 76s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 76s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 76s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 76s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 76s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 76s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 77s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 77s Setting up locales (2.42-2ubuntu5) ... 77s Generating locales (this might take a while)... 79s en_US.UTF-8... done 79s Generation complete. 79s Setting up pollinate (4.33-4ubuntu5) ... 89s Setting up python3-referencing (0.36.2-1ubuntu2) ... 89s Processing triggers for man-db (2.13.1-1) ... 91s Processing triggers for install-info (7.2-5) ... 91s Processing triggers for systemd (259-1ubuntu3) ... 92s autopkgtest [02:31:18]: upgrading testbed (apt dist-upgrade and autopurge) 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Solving dependencies... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s autopkgtest [02:31:24]: rebooting testbed after setup commands that affected boot 144s autopkgtest [02:32:10]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:45:54 UTC 2026 158s autopkgtest [02:32:24]: @@@@@@@@@@@@@@@@@@@@ apt-source bolt-lmm 161s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bolt-lmm 2.4.1+dfsg-2build2 (dsc) [2266 B] 161s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bolt-lmm 2.4.1+dfsg-2build2 (tar) [2805 kB] 161s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bolt-lmm 2.4.1+dfsg-2build2 (diff) [8796 B] 161s gpgv: Signature made Wed Aug 6 15:10:12 2025 UTC 161s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 161s gpgv: Can't check signature: No public key 161s dpkg-source: warning: cannot verify inline signature for ./bolt-lmm_2.4.1+dfsg-2build2.dsc: no acceptable signature found 161s autopkgtest [02:32:27]: testing package bolt-lmm version 2.4.1+dfsg-2build2 162s autopkgtest [02:32:28]: build not needed 164s autopkgtest [02:32:30]: test run-sample-analysis: preparing testbed 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Solving dependencies... 165s The following NEW packages will be installed: 165s bolt-lmm bolt-lmm-example libboost-iostreams1.88.0 165s libboost-program-options1.88.0 libgfortran5 libgomp1 libnlopt0 libopenblas0 165s libopenblas0-pthread 165s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 12.7 MB of archives. 165s After this operation, 44.0 MB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-iostreams1.88.0 ppc64el 1.88.0-1.4ubuntu3 [262 kB] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libboost-program-options1.88.0 ppc64el 1.88.0-1.4ubuntu3 [334 kB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 165s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libnlopt0 ppc64el 2.7.1-7ubuntu1 [292 kB] 165s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 165s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libopenblas0-pthread ppc64el 0.3.30+ds-3 [7966 kB] 165s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libopenblas0 ppc64el 0.3.30+ds-3 [6306 B] 165s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bolt-lmm ppc64el 2.4.1+dfsg-2build2 [347 kB] 166s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bolt-lmm-example all 2.4.1+dfsg-2build2 [2707 kB] 166s Fetched 12.7 MB in 1s (16.0 MB/s) 166s Selecting previously unselected package libboost-iostreams1.88.0:ppc64el. 166s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 82008 files and directories currently installed.) 166s Preparing to unpack .../0-libboost-iostreams1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 166s Unpacking libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 166s Selecting previously unselected package libboost-program-options1.88.0:ppc64el. 166s Preparing to unpack .../1-libboost-program-options1.88.0_1.88.0-1.4ubuntu3_ppc64el.deb ... 166s Unpacking libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 166s Selecting previously unselected package libgomp1:ppc64el. 166s Preparing to unpack .../2-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 166s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 166s Selecting previously unselected package libnlopt0:ppc64el. 166s Preparing to unpack .../3-libnlopt0_2.7.1-7ubuntu1_ppc64el.deb ... 166s Unpacking libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 166s Selecting previously unselected package libgfortran5:ppc64el. 166s Preparing to unpack .../4-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 166s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 166s Selecting previously unselected package libopenblas0-pthread:ppc64el. 166s Preparing to unpack .../5-libopenblas0-pthread_0.3.30+ds-3_ppc64el.deb ... 166s Unpacking libopenblas0-pthread:ppc64el (0.3.30+ds-3) ... 167s Selecting previously unselected package libopenblas0:ppc64el. 167s Preparing to unpack .../6-libopenblas0_0.3.30+ds-3_ppc64el.deb ... 167s Unpacking libopenblas0:ppc64el (0.3.30+ds-3) ... 167s Selecting previously unselected package bolt-lmm. 167s Preparing to unpack .../7-bolt-lmm_2.4.1+dfsg-2build2_ppc64el.deb ... 167s Unpacking bolt-lmm (2.4.1+dfsg-2build2) ... 167s Selecting previously unselected package bolt-lmm-example. 167s Preparing to unpack .../8-bolt-lmm-example_2.4.1+dfsg-2build2_all.deb ... 167s Unpacking bolt-lmm-example (2.4.1+dfsg-2build2) ... 167s Setting up libboost-program-options1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 167s Setting up libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 167s Setting up libboost-iostreams1.88.0:ppc64el (1.88.0-1.4ubuntu3) ... 167s Setting up libgomp1:ppc64el (15.2.0-12ubuntu1) ... 167s Setting up libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 167s Setting up bolt-lmm-example (2.4.1+dfsg-2build2) ... 167s Setting up libopenblas0-pthread:ppc64el (0.3.30+ds-3) ... 167s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 167s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 167s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/powerpc64le-linux-gnu/libopenblas.so.0 (libopenblas.so.0-powerpc64le-linux-gnu) in auto mode 167s Setting up libopenblas0:ppc64el (0.3.30+ds-3) ... 167s Setting up bolt-lmm (2.4.1+dfsg-2build2) ... 167s Processing triggers for man-db (2.13.1-1) ... 167s Processing triggers for libc-bin (2.42-2ubuntu5) ... 184s autopkgtest [02:32:50]: test run-sample-analysis: [----------------------- 185s EUR_subset.bed 185s EUR_subset.bim 185s EUR_subset.dosage.chr17first100 185s EUR_subset.dosage.chr22last100.gz 185s EUR_subset.dosage.indivs 185s EUR_subset.dosage2.chr17first100.gz 185s EUR_subset.dosage2.chr17first100.map 185s EUR_subset.dosage2.chr17second100 185s EUR_subset.dosage2.chr17second100.map 185s EUR_subset.dosage2.chr22last100.gz 185s EUR_subset.dosage2.chr22last100.map 185s EUR_subset.dosage2FileList.txt 185s EUR_subset.exclude 185s EUR_subset.exclude2 185s EUR_subset.fam 185s EUR_subset.impute2.chr17first100.gz 185s EUR_subset.impute2.chr17second100 185s EUR_subset.impute2.chr22last100.gz 185s EUR_subset.impute2.indivs 185s EUR_subset.impute2FileList.txt 185s EUR_subset.modelSnps 185s EUR_subset.modelSnps2 185s EUR_subset.pheno.covars 185s EUR_subset.pheno2.covars 185s EUR_subset.remove 185s example.dosage2Snps.stats 185s example.dosageSnps.stats 185s example.impute2Snps.stats 185s example.log 185s example.stats 185s example_reml2.log 185s run_example.sh 185s run_example_reml2.sh 185s +-----------------------------+ 185s | ___ | 185s | BOLT-LMM, v2.4.1 /_ / | 185s | November 16, 2022 /_/ | 185s | Po-Ru Loh // | 185s | / | 185s +-----------------------------+ 185s 185s Copyright (C) 2014-2022 Harvard University. 185s Distributed under the GNU GPLv3 open source license. 185s 185s Boost version: 1_88 185s 185s Command line options: 185s 185s bolt \ 185s --bfile=EUR_subset \ 185s --remove=EUR_subset.remove \ 185s --exclude=EUR_subset.exclude \ 185s --exclude=EUR_subset.exclude2 \ 185s --phenoFile=EUR_subset.pheno2.covars \ 185s --phenoCol=PHENO \ 185s --covarFile=EUR_subset.pheno2.covars \ 185s --covarCol=CAT_COV \ 185s --qCovarCol=QCOV{1:2} \ 185s --modelSnps=EUR_subset.modelSnps \ 185s --lmm \ 185s --numThreads=2 \ 185s --statsFile=example.stats \ 185s --dosageFile=EUR_subset.dosage.chr17first100 \ 185s --dosageFile=EUR_subset.dosage.chr22last100.gz \ 185s --dosageFidIidFile=EUR_subset.dosage.indivs \ 185s --statsFileDosageSnps=example.dosageSnps.stats \ 185s --impute2FileList=EUR_subset.impute2FileList.txt \ 185s --impute2FidIidFile=EUR_subset.impute2.indivs \ 185s --statsFileImpute2Snps=example.impute2Snps.stats \ 185s --dosage2FileList=EUR_subset.dosage2FileList.txt \ 185s --statsFileDosage2Snps=example.dosage2Snps.stats 185s 185s ERROR: LDscoresFile and LDscoresCol required to calibrate Bayes assoc stats 185s (unless --LDscoresUseChip is set) 185s Aborting due to error processing command line arguments 185s For list of arguments, run with -h (--help) option 185s +-----------------------------+ 185s | ___ | 185s | BOLT-LMM, v2.4.1 /_ / | 185s | November 16, 2022 /_/ | 185s | Po-Ru Loh // | 185s | / | 185s +-----------------------------+ 185s 185s Copyright (C) 2014-2022 Harvard University. 185s Distributed under the GNU GPLv3 open source license. 185s 185s Boost version: 1_88 185s 185s Command line options: 185s 185s bolt \ 185s --bfile=EUR_subset \ 185s --phenoFile=EUR_subset.pheno2.covars \ 185s --exclude=EUR_subset.exclude2 \ 185s --phenoCol=PHENO \ 185s --phenoCol=QCOV1 \ 185s --modelSnps=EUR_subset.modelSnps2 \ 185s --reml \ 185s --numThreads=2 185s 185s Setting number of threads to 2 185s fam: EUR_subset.fam 185s bim(s): EUR_subset.bim 185s bed(s): EUR_subset.bed 185s 185s === Reading genotype data === 185s 185s Total indivs in PLINK data: Nbed = 379 185s Total indivs stored in memory: N = 379 185s Reading bim file #1: EUR_subset.bim 185s Read 54051 snps 185s Total snps in PLINK data: Mbed = 54051 185s Reading exclude file (SNPs to exclude): EUR_subset.exclude2 185s Excluded 47959 SNP(s) 185s Reading list of SNPs to include in model (i.e., GRM): EUR_subset.modelSnps2 185s WARNING: SNP has been excluded: rs2176153 185s WARNING: SNP has been excluded: rs77036651 185s WARNING: SNP has been excluded: rs189917831 185s WARNING: SNP has been excluded: rs76452819 185s WARNING: SNP has been excluded: rs77203822 185s Included 1331 SNP(s) in model in 2 variance component(s) 185s WARNING: 10420 SNP(s) had been excluded 185s 185s Breakdown of SNP pre-filtering results: 185s 1331 SNPs to include in model (i.e., GRM) 185s 0 additional non-GRM SNPs loaded 185s 52720 excluded SNPs 185s Allocating 1331 x 380/4 bytes to store genotypes 185s Reading genotypes and performing QC filtering on snps and indivs... 185s Reading bed file #1: EUR_subset.bed 185s Expecting 5134845 (+3) bytes for 379 indivs, 54051 snps 185s Total indivs after QC: 379 185s Total post-QC SNPs: M = 1331 185s Variance component 1: 660 post-QC SNPs (name: 'chr21') 185s Variance component 2: 671 post-QC SNPs (name: 'chr22') 185s Time for SnpData setup = 0.243644 sec 185s 185s === Reading phenotype and covariate data === 185s 185s Read data for 373 indivs (ignored 0 without genotypes) from: 185s EUR_subset.pheno2.covars 185s Number of indivs with no missing phenotype(s) to use: 369 185s NOTE: Using all-1s vector (constant term) in addition to specified covariates 185s Using quantitative covariate: CONST_ALL_ONES 185s Number of individuals used in analysis: Nused = 369 185s Singular values of covariate matrix: 185s S[0] = 19.2094 185s Total covariate vectors: C = 1 185s Total independent covariate vectors: Cindep = 1 185s 185s === Initializing Bolt object: projecting and normalizing SNPs === 185s 185s Number of chroms with >= 1 good SNP: 2 185s Average norm of projected SNPs: 368.000000 185s Dimension of all-1s proj space (Nused-1): 368 185s Time for covariate data setup + Bolt initialization = 0.0056181 sec 185s 185s Phenotype 1: N = 369 mean = -0.000706532 std = 1.02606 185s Phenotype 2: N = 369 mean = 1.53117 std = 0.499705 185s 185s === Estimating variance parameters === 185s 185s === Making initial guesses for phenotype 1 === 185s 185s Using 3 random trials 185s 185s Estimating MC scaling f_REML at log(delta) = 1.09861, h2 = 0.25... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.1,0.2) res2s: 793.48..209.284 185s iter 2: time=0.00 rNorms/orig: (0.02,0.05) res2s: 852.844..224.032 185s iter 3: time=0.00 rNorms/orig: (0.004,0.009) res2s: 855.812..225.515 185s iter 4: time=0.00 rNorms/orig: (0.001,0.002) res2s: 855.998..225.607 185s iter 5: time=0.00 rNorms/orig: (0.0002,0.0002) res2s: 856.011..225.61 185s Converged at iter 5: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 36.7%, memory/overhead = 63.3% 185s MCscaling: logDelta = 1.10, h2 = 0.250, f = -0.0360561 185s 185s Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.08,0.09) res2s: 2291.49..290.653 185s iter 2: time=0.00 rNorms/orig: (0.006,0.01) res2s: 2334.07..296.495 185s iter 3: time=0.00 rNorms/orig: (0.0005,0.001) res2s: 2334.71..296.683 185s iter 4: time=0.00 rNorms/orig: (5e-05,0.0001) res2s: 2334.72..296.687 185s Converged at iter 4: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.2%, memory/overhead = 59.8% 185s MCscaling: logDelta = 1.95, h2 = 0.125, f = 0.013492 185s 185s Estimating MC scaling f_REML at log(delta) = 1.71519, h2 = 0.152492... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.09,0.1) res2s: 1743.02..271.466 185s iter 2: time=0.00 rNorms/orig: (0.009,0.02) res2s: 1791.41..279.33 185s iter 3: time=0.00 rNorms/orig: (0.0009,0.002) res2s: 1792.43..279.685 185s iter 4: time=0.00 rNorms/orig: (0.0001,0.0003) res2s: 1792.47..279.694 185s Converged at iter 4: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 39.5%, memory/overhead = 60.5% 185s MCscaling: logDelta = 1.72, h2 = 0.152, f = 0.00193922 185s 185s Estimating MC scaling f_REML at log(delta) = 1.67646, h2 = 0.157565... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.09,0.1) res2s: 1663.2..268.006 185s iter 2: time=0.00 rNorms/orig: (0.009,0.02) res2s: 1712.52..276.249 185s iter 3: time=0.00 rNorms/orig: (0.001,0.003) res2s: 1713.63..276.64 185s iter 4: time=0.00 rNorms/orig: (0.0001,0.0003) res2s: 1713.67..276.651 185s Converged at iter 4: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.0%, memory/overhead = 60.0% 185s MCscaling: logDelta = 1.68, h2 = 0.158, f = -0.000137788 185s 185s Secant iteration for h2 estimation converged in 2 steps 185s Estimated (pseudo-)heritability: h2g = 0.158 185s To more precisely estimate variance parameters and estimate s.e., use --reml 185s Variance params: sigma^2_K = 0.165577, logDelta = 1.676462, f = -0.000137788 185s 185s h2 with all VCs: 0.157565 185s 185s === Re-estimating variance parameters for 2 leave-out reps === 185s 185s Using 3 random trials 185s 185s Estimating MC scaling f_REML at log(delta) = 1.67646, h2 = 0.157565... 185s Batch-solving 8 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.1,0.2) res2s: 1725.01..276.852 185s iter 2: time=0.00 rNorms/orig: (0.02,0.03) res2s: 1818.96..289.755 185s iter 3: time=0.00 rNorms/orig: (0.003,0.005) res2s: 1822.44..290.383 185s iter 4: time=0.00 rNorms/orig: (0.0006,0.0008) res2s: 1822.54..290.41 185s iter 5: time=0.00 rNorms/orig: (8e-05,0.0001) res2s: 1822.54..290.411 185s Converged at iter 5: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 43.9%, memory/overhead = 56.1% 185s Estimating MC scaling f_REML at log(delta) = 2.67646, h2 = 0.0643767... 185s Batch-solving 8 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.06,0.06) res2s: 5347.92..340.104 185s iter 2: time=0.00 rNorms/orig: (0.003,0.006) res2s: 5396.21..343.074 185s iter 3: time=0.00 rNorms/orig: (0.0002,0.0004) res2s: 5396.58..343.106 185s Converged at iter 3: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 43.6%, memory/overhead = 56.4% 185s WARNING: Estimated h2 on leave-out batch 0 exceeds all-SNPs h2 185s Replacing 0.189722 with 0.157565 185s MCscaling: logDelta[0] = 1.676462, h2 = 0.158, Mused = 671 (50.4%) 185s MCscaling: logDelta[1] = 4.079406, h2 = 0.017, Mused = 660 (49.6%) 185s 185s h2 leaving out VC 1: 0.157565 185s h2 leaving out VC 2: 0.0166361 185s guess h2 for VC 1: 0.0150473 185s guess h2 for VC 2: 0.142517 185s === Making initial guesses for phenotype 2 === 185s 185s Using 3 random trials 185s 185s Estimating MC scaling f_REML at log(delta) = 1.09861, h2 = 0.25... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.1,0.2) res2s: 793.48..51.8247 185s iter 2: time=0.00 rNorms/orig: (0.02,0.05) res2s: 852.844..54.9262 185s iter 3: time=0.00 rNorms/orig: (0.004,0.008) res2s: 855.812..55.1839 185s iter 4: time=0.00 rNorms/orig: (0.001,0.002) res2s: 855.998..55.2016 185s iter 5: time=0.00 rNorms/orig: (0.0002,0.0002) res2s: 856.011..55.2022 185s Converged at iter 5: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 39.7%, memory/overhead = 60.3% 185s MCscaling: logDelta = 1.10, h2 = 0.250, f = -0.0981326 185s 185s Estimating MC scaling f_REML at log(delta) = 1.94591, h2 = 0.125... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.08,0.09) res2s: 2291.49..70.4467 185s iter 2: time=0.00 rNorms/orig: (0.006,0.01) res2s: 2334.07..71.6106 185s iter 3: time=0.00 rNorms/orig: (0.0005,0.001) res2s: 2334.71..71.6417 185s iter 4: time=0.00 rNorms/orig: (5e-05,0.0001) res2s: 2334.72..71.6423 185s Converged at iter 4: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.3%, memory/overhead = 59.7% 185s MCscaling: logDelta = 1.95, h2 = 0.125, f = -0.0575396 185s 185s Estimating MC scaling f_REML at log(delta) = 3.14694, h2 = 0.0412122... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.02,0.03) res2s: 8577.73..84.51 185s iter 2: time=0.00 rNorms/orig: (0.0007,0.001) res2s: 8594.5..84.675 185s iter 3: time=0.00 rNorms/orig: (2e-05,6e-05) res2s: 8594.54..84.6756 185s Converged at iter 3: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.3%, memory/overhead = 59.7% 185s MCscaling: logDelta = 3.15, h2 = 0.041, f = -0.0249719 185s 185s Estimating MC scaling f_REML at log(delta) = 4.06784, h2 = 0.0168263... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.01,0.01) res2s: 22267.1..88.8409 185s iter 2: time=0.00 rNorms/orig: (0.0001,0.0002) res2s: 22274.2..88.8706 185s Converged at iter 2: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.8%, memory/overhead = 59.2% 185s MCscaling: logDelta = 4.07, h2 = 0.017, f = -0.0129428 185s 185s Estimating MC scaling f_REML at log(delta) = 5.0587, h2 = 0.00631367... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.004,0.004) res2s: 60906.5..90.7409 185s iter 2: time=0.00 rNorms/orig: (2e-05,3e-05) res2s: 60909.2..90.7452 185s Converged at iter 2: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 39.7%, memory/overhead = 60.3% 185s MCscaling: logDelta = 5.06, h2 = 0.006, f = -0.00650698 185s 185s Estimating MC scaling f_REML at log(delta) = 6.06052, h2 = 0.00232776... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.001,0.002) res2s: 167006..91.4665 185s iter 2: time=0.00 rNorms/orig: (2e-06,4e-06) res2s: 167007..91.4671 185s Converged at iter 2: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 40.3%, memory/overhead = 59.7% 185s MCscaling: logDelta = 6.06, h2 = 0.002, f = -0.00335926 185s 185s Estimating MC scaling f_REML at log(delta) = 7.12966, h2 = 0.000800349... 185s Batch-solving 4 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.0005,0.0005) res2s: 488117..91.7453 185s iter 2: time=0.00 rNorms/orig: (3e-07,5e-07) res2s: 488117..91.7454 185s Converged at iter 2: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 39.8%, memory/overhead = 60.2% 185s MCscaling: logDelta = 7.13, h2 = 0.001, f = -0.00171823 185s 185s WARNING: Secant iteration for h2 estimation may not have converged 185s Estimated (pseudo-)heritability: h2g = 0.001 185s To more precisely estimate variance parameters and estimate s.e., use --reml 185s Variance params: sigma^2_K = 0.000200, logDelta = 7.129662, f = -0.00171823 185s 185s h2 with all VCs: 0.000800349 185s 185s === Re-estimating variance parameters for 2 leave-out reps === 185s 185s Using 3 random trials 185s 185s Estimating MC scaling f_REML at log(delta) = 7.12966, h2 = 0.000800349... 185s Batch-solving 8 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.0007,0.0008) res2s: 489414..91.7367 185s iter 2: time=0.00 rNorms/orig: (5e-07,8e-07) res2s: 489415..91.7369 185s Converged at iter 2: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 43.5%, memory/overhead = 56.5% 185s Estimating MC scaling f_REML at log(delta) = 8.12966, h2 = 0.000294581... 185s Batch-solving 8 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.0002,0.0003) res2s: 1.33099e+06..91.8346 185s Converged at iter 1: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 43.7%, memory/overhead = 56.3% 185s MCscaling: logDelta[0] = 41.354963, h2 = 0.000, Mused = 671 (50.4%) 185s WARNING: Estimated h2 on leave-out batch 1 exceeds all-SNPs h2 185s Replacing 1 with 0.000800349 185s MCscaling: logDelta[1] = 7.129662, h2 = 0.001, Mused = 660 (49.6%) 185s 185s h2 leaving out VC 1: 1e-09 185s h2 leaving out VC 2: 0.000800349 185s guess h2 for VC 1: 0.000800348 185s guess h2 for VC 2: 9.99999e-10 (setting to 1e-09) 185s 185s =============================================================================== 185s 185s Stochastic REML optimization with MCtrials = 15 185s 185s phenoNormsCorrs[2,2]((1.02606,0.0479548),(0.0479548,0.499705)) 185s Initial variance parameter guesses: 185s Vegs[0][2,2]((0.842435,0.0439974),(0.0439974,0.9992)) 185s Vegs[1][2,2]((0.0150473,0.000166418),(0.000166418,0.000800348)) 185s Vegs[2][2,2]((0.142517,5.72488e-07),(5.72488e-07,1e-09)) 185s 185s Performing initial gradient evaluation 185s Batch-solving 16 systems of equations using conjugate gradient iteration 185s iter 1: time=0.01 rNorms/orig: (0.09,0.1) res2s: 760.925..714.309 185s iter 2: time=0.01 rNorms/orig: (0.01,0.02) res2s: 778.935..735.897 185s iter 3: time=0.01 rNorms/orig: (0.002,0.004) res2s: 779.658..737.32 185s iter 4: time=0.01 rNorms/orig: (0.0002,0.0005) res2s: 779.68..737.382 185s iter 5: time=0.01 rNorms/orig: (5e-05,7e-05) res2s: 779.68..737.383 185s Converged at iter 5: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 68.6%, memory/overhead = 31.4% 185s grad[9](-1.30941,-10.6066,2.32453,-12.4479,11.8131,11.8748,8.81056,-14.0363,-10.9614) 185s 185s ------------------------------------------------------------------------------- 185s 185s Start ITER 1: computing AI matrix 185s Multiplying solutions by variance components... time=0.00 185s Batch-solving 9 systems of equations using conjugate gradient iteration 185s iter 1: time=0.00 rNorms/orig: (0.04,0.2) res2s: 374.999..574.247 185s iter 2: time=0.00 rNorms/orig: (0.005,0.03) res2s: 391.745..576.984 185s iter 3: time=0.00 rNorms/orig: (0.0009,0.004) res2s: 392.536..577.046 185s iter 4: time=0.00 rNorms/orig: (0.0001,0.0006) res2s: 392.567..577.049 185s iter 5: time=0.00 rNorms/orig: (2e-05,9e-05) res2s: 392.568..577.049 185s Converged at iter 5: rNorms/orig all < CGtol=0.0005 185s Time breakdown: dgemm = 60.9%, memory/overhead = 39.1% 186s 186s Constrained Newton-Raphson optimized variance parameters: 186s optVegs[0][2,2]((0.765158,-0.00572469),(-0.00572469,0.933015)) 186s optVegs[1][2,2]((0.0153481,0.0330912),(0.0330912,0.0713461)) 186s optVegs[2][2,2]((0.22019,-0.0137448),(-0.0137448,0.00085799)) 186s 186s Predicted change in log likelihood: 1.37468 186s 186s Computing actual (approximate) change in log likelihood 186s Batch-solving 16 systems of equations using conjugate gradient iteration 186s iter 1: time=0.01 rNorms/orig: (0.1,0.2) res2s: 750.649..696.829 186s iter 2: time=0.01 rNorms/orig: (0.03,0.05) res2s: 788.584..740.822 186s iter 3: time=0.01 rNorms/orig: (0.005,0.01) res2s: 791.331..745.887 186s iter 4: time=0.01 rNorms/orig: (0.001,0.002) res2s: 791.526..746.312 186s iter 5: time=0.01 rNorms/orig: (0.0002,0.0004) res2s: 791.541..746.336 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 68.4%, memory/overhead = 31.6% 186s grad[9](1.05495,2.07853,0.998772,-10.7428,11.8466,-0.472294,0.619778,-0.268081,-9.76099) 186s 186s Approximate change in log likelihood: 1.35574 (attempt 1) 186s rho (approximate / predicted change in LL) = 0.986222 186s Old trust region radius: 1e+100 186s New trust region radius: 1e+100 186s Accepted step 186s 186s End ITER 1 186s Vegs[0][2,2]((0.765158,-0.00572469),(-0.00572469,0.933015)) 186s Vegs[1][2,2]((0.0153481,0.0330912),(0.0330912,0.0713461)) 186s Vegs[2][2,2]((0.22019,-0.0137448),(-0.0137448,0.00085799)) 186s 186s ------------------------------------------------------------------------------- 186s 186s Start ITER 2: computing AI matrix 186s Multiplying solutions by variance components... time=0.00 186s Batch-solving 9 systems of equations using conjugate gradient iteration 186s iter 1: time=0.00 rNorms/orig: (0.07,0.2) res2s: 407.326..557.419 186s iter 2: time=0.00 rNorms/orig: (0.009,0.06) res2s: 439.301..565.84 186s iter 3: time=0.00 rNorms/orig: (0.003,0.01) res2s: 441.974..566.081 186s iter 4: time=0.00 rNorms/orig: (0.0005,0.002) res2s: 442.184..566.102 186s iter 5: time=0.00 rNorms/orig: (0.0001,0.0004) res2s: 442.196..566.103 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 60.7%, memory/overhead = 39.3% 186s Reducing off-diagonals by a factor of 4.65661e-09 to make matrix positive definite 186s Reducing off-diagonals by a factor of 6.33299e-07 to make matrix positive definite 186s 186s Constrained Newton-Raphson optimized variance parameters: 186s optVegs[0][2,2]((0.771913,0.00133026),(0.00133026,0.932468)) 186s optVegs[1][2,2]((0.0143745,0.0334318),(0.0334318,0.0777549)) 186s optVegs[2][2,2]((0.219274,-0.0159986),(-0.0159986,0.00116729)) 186s 186s Predicted change in log likelihood: 0.0154668 186s 186s Computing actual (approximate) change in log likelihood 186s Batch-solving 16 systems of equations using conjugate gradient iteration 186s iter 1: time=0.01 rNorms/orig: (0.1,0.2) res2s: 746.437..688.903 186s iter 2: time=0.01 rNorms/orig: (0.03,0.05) res2s: 784.68..732.913 186s iter 3: time=0.01 rNorms/orig: (0.005,0.01) res2s: 787.368..737.856 186s iter 4: time=0.01 rNorms/orig: (0.0009,0.002) res2s: 787.557..738.266 186s iter 5: time=0.01 rNorms/orig: (0.0002,0.0004) res2s: 787.572..738.289 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 68.1%, memory/overhead = 31.9% 186s grad[9](0.00591724,-0.0085285,-0.028017,-11.5488,9.81765,-2.08834,-0.0579192,-1.65527,-10.548) 186s 186s Approximate change in log likelihood: 0.0157246 (attempt 1) 186s rho (approximate / predicted change in LL) = 1.01667 186s Old trust region radius: 1e+100 186s New trust region radius: 1e+100 186s Accepted step 186s 186s End ITER 2 186s Vegs[0][2,2]((0.771913,0.00133026),(0.00133026,0.932468)) 186s Vegs[1][2,2]((0.0143745,0.0334318),(0.0334318,0.0777549)) 186s Vegs[2][2,2]((0.219274,-0.0159986),(-0.0159986,0.00116729)) 186s 186s ------------------------------------------------------------------------------- 186s 186s Start ITER 3: computing AI matrix 186s Multiplying solutions by variance components... time=0.00 186s Batch-solving 9 systems of equations using conjugate gradient iteration 186s iter 1: time=0.00 rNorms/orig: (0.08,0.2) res2s: 398.265..544.496 186s iter 2: time=0.00 rNorms/orig: (0.01,0.06) res2s: 429.399..553.751 186s iter 3: time=0.00 rNorms/orig: (0.003,0.01) res2s: 431.977..554.012 186s iter 4: time=0.00 rNorms/orig: (0.0005,0.002) res2s: 432.177..554.032 186s iter 5: time=0.00 rNorms/orig: (0.0001,0.0004) res2s: 432.188..554.033 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 61.1%, memory/overhead = 38.9% 186s Reducing off-diagonals by a factor of 9.31323e-10 to make matrix positive definite 186s 186s Constrained Newton-Raphson optimized variance parameters: 186s optVegs[0][2,2]((0.772095,0.00170122),(0.00170122,0.931973)) 186s optVegs[1][2,2]((0.0142293,0.0333333),(0.0333333,0.0780861)) 186s optVegs[2][2,2]((0.219249,-0.0163614),(-0.0163614,0.00122097)) 186s 186s Predicted change in log likelihood: 4.02471e-05 186s AI iteration converged: predicted change in log likelihood < tol = 0.01 186s 186s =============================================================================== 186s 186s Refining REML optimization with MCtrials = 100 186s 186s phenoNormsCorrs[2,2]((1.02606,0.0479548),(0.0479548,0.499705)) 186s Initial variance parameter guesses: 186s Vegs[0][2,2]((0.772095,0.00170122),(0.00170122,0.931973)) 186s Vegs[1][2,2]((0.0142293,0.0333333),(0.0333333,0.0780861)) 186s Vegs[2][2,2]((0.219249,-0.0163614),(-0.0163614,0.00122097)) 186s 186s Performing initial gradient evaluation 186s Batch-solving 101 systems of equations using conjugate gradient iteration 186s iter 1: time=0.02 rNorms/orig: (0.1,0.2) res2s: 706.483..688.969 186s iter 2: time=0.02 rNorms/orig: (0.03,0.05) res2s: 747.476..733.008 186s iter 3: time=0.02 rNorms/orig: (0.005,0.01) res2s: 750.072..737.945 186s iter 4: time=0.02 rNorms/orig: (0.0009,0.002) res2s: 750.222..738.355 186s iter 5: time=0.02 rNorms/orig: (0.0002,0.0004) res2s: 750.234..738.377 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 62.1%, memory/overhead = 37.9% 186s grad[9](-0.481154,11.4584,-2.77161,-10.4154,13.8913,-6.57445,-1.85262,8.14534,-15.325) 186s 186s ------------------------------------------------------------------------------- 186s 186s Start ITER 1: computing AI matrix 186s Multiplying solutions by variance components... time=0.00 186s Batch-solving 9 systems of equations using conjugate gradient iteration 186s iter 1: time=0.00 rNorms/orig: (0.08,0.2) res2s: 398.208..544.689 186s iter 2: time=0.00 rNorms/orig: (0.01,0.06) res2s: 429.336..554.021 186s iter 3: time=0.00 rNorms/orig: (0.003,0.01) res2s: 431.914..554.281 186s iter 4: time=0.00 rNorms/orig: (0.0005,0.002) res2s: 432.113..554.3 186s iter 5: time=0.00 rNorms/orig: (0.0001,0.0004) res2s: 432.124..554.301 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 61.2%, memory/overhead = 38.8% 186s Reducing off-diagonals by a factor of 5.58794e-09 to make matrix positive definite 186s Reducing off-diagonals by a factor of 9.31323e-09 to make matrix positive definite 186s Reducing off-diagonals by a factor of 9.49949e-07 to make matrix positive definite 186s 186s Constrained Newton-Raphson optimized variance parameters: 186s optVegs[0][2,2]((0.785365,0.040372),(0.040372,0.934999)) 186s optVegs[1][2,2]((0.00797118,0.0213014),(0.0213014,0.0569236)) 186s optVegs[2][2,2]((0.205337,-0.0137552),(-0.0137552,0.000921438)) 186s 186s Predicted change in log likelihood: 0.259597 186s 186s Computing actual (approximate) change in log likelihood 186s Batch-solving 101 systems of equations using conjugate gradient iteration 186s iter 1: time=0.02 rNorms/orig: (0.1,0.2) res2s: 714.215..707.745 186s iter 2: time=0.02 rNorms/orig: (0.03,0.05) res2s: 752.267..749.652 186s iter 3: time=0.02 rNorms/orig: (0.004,0.01) res2s: 754.608..754.208 186s iter 4: time=0.02 rNorms/orig: (0.0008,0.002) res2s: 754.711..754.561 186s iter 5: time=0.02 rNorms/orig: (0.0001,0.0003) res2s: 754.717..754.578 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 62.8%, memory/overhead = 37.2% 186s grad[9](0.0523622,-0.515852,0.17233,-8.95624,6.92966,-0.795789,0.171247,-1.57789,-12.8267) 186s 186s Approximate change in log likelihood: 0.242613 (attempt 1) 186s rho (approximate / predicted change in LL) = 0.934576 186s Old trust region radius: 1e+100 186s New trust region radius: 1e+100 186s Accepted step 186s 186s End ITER 1 186s Vegs[0][2,2]((0.785365,0.040372),(0.040372,0.934999)) 186s Vegs[1][2,2]((0.00797118,0.0213014),(0.0213014,0.0569236)) 186s Vegs[2][2,2]((0.205337,-0.0137552),(-0.0137552,0.000921438)) 186s 186s ------------------------------------------------------------------------------- 186s 186s Start ITER 2: computing AI matrix 186s Multiplying solutions by variance components... time=0.00 186s Batch-solving 9 systems of equations using conjugate gradient iteration 186s iter 1: time=0.00 rNorms/orig: (0.07,0.2) res2s: 402.764..584.106 186s iter 2: time=0.00 rNorms/orig: (0.01,0.06) res2s: 433.908..591.264 186s iter 3: time=0.00 rNorms/orig: (0.002,0.01) res2s: 436.366..591.44 186s iter 4: time=0.00 rNorms/orig: (0.0004,0.002) res2s: 436.537..591.455 186s iter 5: time=0.00 rNorms/orig: (7e-05,0.0004) res2s: 436.546..591.455 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 60.3%, memory/overhead = 39.7% 186s Reducing off-diagonals by a factor of 2.0396e-07 to make matrix positive definite 186s Reducing off-diagonals by a factor of 9.31323e-10 to make matrix positive definite 186s 186s Constrained Newton-Raphson optimized variance parameters: 186s optVegs[0][2,2]((0.783492,0.0363805),(0.0363805,0.933612)) 186s optVegs[1][2,2]((0.00876578,0.0228395),(0.0228395,0.0595087)) 186s optVegs[2][2,2]((0.20701,-0.012213),(-0.012213,0.000720534)) 186s 186s Predicted change in log likelihood: 0.00192689 186s 186s Computing actual (approximate) change in log likelihood 186s Batch-solving 101 systems of equations using conjugate gradient iteration 186s iter 1: time=0.02 rNorms/orig: (0.1,0.2) res2s: 713.652..706.286 186s iter 2: time=0.02 rNorms/orig: (0.03,0.05) res2s: 752.336..748.698 186s iter 3: time=0.02 rNorms/orig: (0.004,0.01) res2s: 754.705..753.319 186s iter 4: time=0.02 rNorms/orig: (0.0008,0.002) res2s: 754.815..753.681 186s iter 5: time=0.02 rNorms/orig: (0.0001,0.0004) res2s: 754.823..753.699 186s Converged at iter 5: rNorms/orig all < CGtol=0.0005 186s Time breakdown: dgemm = 62.8%, memory/overhead = 37.2% 186s grad[9](0.0251488,0.0705356,0.0152875,-9.10247,7.00093,-1.39784,-0.0428011,-1.50464,-12.9334) 186s 186s Approximate change in log likelihood: 0.00170722 (attempt 1) 186s rho (approximate / predicted change in LL) = 0.885997 186s Old trust region radius: 1e+100 186s New trust region radius: 1e+100 186s Accepted step 186s 186s End ITER 2 186s Vegs[0][2,2]((0.783492,0.0363805),(0.0363805,0.933612)) 186s Vegs[1][2,2]((0.00876578,0.0228395),(0.0228395,0.0595087)) 186s Vegs[2][2,2]((0.20701,-0.012213),(-0.012213,0.000720534)) 186s 186s ------------------------------------------------------------------------------- 186s 186s Start ITER 3: computing AI matrix 186s Multiplying solutions by variance components... time=0.00 186s Batch-solving 9 systems of equations using conjugate gradient iteration 186s iter 1: time=0.00 rNorms/orig: (0.07,0.2) res2s: 402.597..582.684 186s iter 2: time=0.00 rNorms/orig: (0.01,0.06) res2s: 433.859..590.233 187s iter 3: time=0.00 rNorms/orig: (0.003,0.01) res2s: 436.334..590.44 187s iter 4: time=0.00 rNorms/orig: (0.0004,0.002) res2s: 436.509..590.457 187s iter 5: time=0.00 rNorms/orig: (7e-05,0.0004) res2s: 436.518..590.457 187s Converged at iter 5: rNorms/orig all < CGtol=0.0005 187s Time breakdown: dgemm = 60.2%, memory/overhead = 39.8% 187s Reducing off-diagonals by a factor of 6.51926e-09 to make matrix positive definite 187s Reducing off-diagonals by a factor of 9.31323e-10 to make matrix positive definite 187s 187s Constrained Newton-Raphson optimized variance parameters: 187s optVegs[0][2,2]((0.783819,0.0368325),(0.0368325,0.934147)) 187s optVegs[1][2,2]((0.00867992,0.0226326),(0.0226326,0.0590136)) 187s optVegs[2][2,2]((0.206868,-0.0122978),(-0.0122978,0.000731076)) 187s 187s Predicted change in log likelihood: 3.57586e-05 187s AI iteration converged: predicted change in log likelihood < tol = 0.0001 187s 187s AIinv[9,9]((0.0168316,0.000217188,3.82762e-05,-0.00712081,0.000244769,-3.27396e-05,-0.00690898,-0.000254327,-6.38159e-06),(0.000217188,0.00889807,0.000113791,8.62834e-05,-0.00346643,0.00030023,-7.30933e-05,-0.00367126,-0.000179581),(3.82762e-05,0.000113791,0.0186891,-3.47388e-05,8.37372e-05,-0.00668092,1.22012e-06,8.1478e-05,-0.007825),(-0.00712081,8.62834e-05,-3.47388e-05,0.00771484,2.67737e-05,5.51736e-05,-0.000126783,-7.76762e-05,-6.4167e-06),(0.000244769,-0.00346643,8.37372e-05,2.67737e-05,0.00368039,8.94718e-05,-0.000271268,6.45816e-05,-0.000116576),(-3.27396e-05,0.00030023,-0.00668092,5.51736e-05,8.94718e-05,0.00709772,-1.13905e-05,-0.000385076,0.000265777),(-0.00690898,-7.30933e-05,1.22012e-06,-0.000126783,-0.000271268,-1.13905e-05,0.00939074,0.000348365,1.17676e-05),(-0.000254327,-0.00367126,8.1478e-05,-7.76762e-05,6.45816e-05,-0.000385076,0.000348365,0.00429575,0.000264962),(-6.38159e-06,-0.000179581,-0.007825,-6.4167e-06,-0.000116576,0.000265777,1.17676e-05,0.000264962,0.00807996)) 187s 187s Variance component 0: [2,2]((0.783819,0.0368325),(0.0368325,0.934147)) 187s entry (1,1): 0.783819 (0.129737) 187s entry (1,2): 0.036832 (0.094330) corr (1,2): 0.043044 187s entry (2,2): 0.934147 (0.136708) 187s Variance component 1: [2,2]((0.00867992,0.0226326),(0.0226326,0.0590136)) 187s entry (1,1): 0.008680 (0.087834) 187s entry (1,2): 0.022633 (0.060666) corr (1,2): 1.000000 187s entry (2,2): 0.059014 (0.084248) 187s Variance component 2: [2,2]((0.206868,-0.0122978),(-0.0122978,0.000731076)) 187s entry (1,1): 0.206868 (0.096906) 187s entry (1,2): -0.012298 (0.065542) corr (1,2): -0.999999 187s entry (2,2): 0.000731 (0.089889) 187s 187s Phenotype 1 variance sigma2: 1.052130 (0.078953) 187s Phenotype 2 variance sigma2: 0.248180 (0.027530) 187s 187s Variance component 0: (environment/noise) 187s h2e (1,1): 0.784316 (0.126789) 187s resid corr (1,2): 0.043044 (0.110800) 187s h2e (2,2): 0.939888 (0.126230) 187s Variance component 1: "chr21" 187s h2g (1,1): 0.008685 (0.088284) 187s gen corr (1,2): 1.000000 (5.785865) 187s h2g (2,2): 0.059376 (0.084815) 187s Variance component 2: "chr22" 187s h2g (1,1): 0.206999 (0.093565) 187s gen corr (1,2): -0.999999 (62.256618) 187s h2g (2,2): 0.000736 (0.090888) 187s 187s Total elapsed time for analysis = 1.78438 sec 187s autopkgtest [02:32:53]: test run-sample-analysis: -----------------------] 187s autopkgtest [02:32:53]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 187s run-sample-analysis PASS 188s autopkgtest [02:32:54]: @@@@@@@@@@@@@@@@@@@@ summary 188s run-sample-analysis PASS